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Open Access Highly Accessed Research article

Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

Kassa Semagn1*, Cosmos Magorokosho2, Bindiganavile S Vivek3, Dan Makumbi1, Yoseph Beyene1, Stephen Mugo1, BM Prasanna1 and Marilyn L Warburton4

Author Affiliations

1 International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market 00621, Nairobi, Kenya

2 CIMMYT, 12.5 Km peg Mazowe Road, P.O. Box MP163, Mount Pleasant, Harare, Zimbabwe

3 CIMMYT, C/o ICRISAT, Patancheru 502324, India

4 United States Department of Agriculture-Agricultural Research Service: Corn Host Plant Resistance Research Unit, Box 9555, Mississippi State, MS 39762, USA

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BMC Genomics 2012, 13:113  doi:10.1186/1471-2164-13-113

Published: 25 March 2012

Abstract

Background

Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays.

Results

Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays.

Conclusions

There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.